Mass Effect: Changed
by Kraretyer
Summary: Shepard died that day when the Collectors attacked the Normandy SR1. He was rebuilt, but is he truly the same person he was? Will he rediscover his humanity and find something,or someone, that is worth fighting for again?
1. Chapter 1-The Beginning

Author's Note:

Hi, all. First off, I'd like to mention that this is my first fanfic. Reviews, both positive and negative, are appreciated. I've always been a fan of Mass Effect, and decided to write this purely for entertainment. I already have ideas for a continuation, with my own plot twists in the story. I'll continue if enough people show interest.

Disclaimer: I do not own Mass Effect, any of its characters, races, locations, insignia, etc. They are the property of Bioware.

Anyway, enjoy.

~Kraretyer

He ran.

He ran through fire and smoke, through the red haze that threatened to suffocate him. Alarm klaxons blared their wailing song as the ship shuddered under the assault.

Another explosion rocked the ship and sent him flying forwards. His armor screeched as he returned to the deck, skidding along the floor before he recovered and continued running.

He faltered as he ran into the CIC. The entire ceiling, and much of the opposite wall, had been ripped away and now showed a breathtaking view of the stars, and the planet nearby. The man moved as fast as he could, careful to have one foot connected to the deck whenever another was not, lest he lose traction and float away. Past the galaxy map, past the broken stations, past twisted metal, past the bodies floating silently in the zero gravity.

He reached the pilot's helm and passed through the transparent barrier between the compartment and empty space.

"Joker!" He shouted at the seated figure gesturing desperately on a holographic interface.

The armored man lurched forward as another explosion rocked the ship, steadying himself on the back of the pilot's seat.

"Come on, Joker. We have to get out of here," He said.

"No! I won't abandon the Normandy!" Joker replied, "I can still save her!"

"The Normandy is gone, Joker, Just like we'll be if we don't get the hell out of here!" The man said firmly.

"No! I can…oh no. It's coming around for another attack!"

Suddenly an intense beam of light struck into the space behind the two of them. The armored man looked back to see it cut through the deck plates like it was nothing. He ran back to the cockpit and grabbed Joker's arm. He winced in pain and told him to watch the arm as the man half-carried him towards the nearby escape pod.

He deposited Joker in the pod just as the beam struck the ship again, knocking him backwards, away from the pod. It now occupied the space between the two of them. He grabbed onto the wall panel with the release mechanism as he floated past and smashed his fist onto the button.

"Shepard!" Joker cried as the pod doors closed, sealing both their fates.

Shepard lost his grip on the panel and floated through the vacuum before another explosion flung him into a bulkhead. He rebounded and began floating into empty space.

He was unable to control his movement as he watched the mysterious ship carve the Normandy apart, explosions raking her hull under the merciless alien onslaught. Shepard thought he almost heard a groan as the ship surrendered and finally blew apart.

He watched the debris shoot around him and suddenly clutched the place where his helmet joined his suit, seeing and feeling the air in his suit bleed out into the void. He frantically reached back and tried to stem the flow of gases, his body thrashing in the empty space as he fought to live. As he felt the last of his oxygen leave him, one thought occupied his mind.

Sorrow.

Sorrow that he had never told her how he felt.

And now it was too late.

As the darkness engulfed him, he uttered one thing into the void.

"I'm sorry"

If you're wondering, I do plan to add the romance in future chapters, along with many different plot twists.


	2. Chapter 2-Rebirth

**A/N: So here is the second chapter. I must have gone through it half a dozen times checking for errors and grammar mistakes, but I hope the result is something you'll enjoy. Again, reviews are welcome.**

**~Kraretyer**

* * *

He was lying in a forest.

He didn't remember anything. It was a curious feeling, to have no memory. Try as he might, he couldn't even remember his own name. He slowly rose from the ground and surveyed his surroundings.

Fog hung in the air like a cloud. The trees stood forlornly reaching into a sky he couldn't see. What sparse vegetation there was clustered around the trees, as if seeking shelter. The eeriest part was the silence, not the lack of any noise, but the intense feeling that it was missing. A wind blew through, blowing leaves past him, but he could not feel it.

"Hello?" He called.

The only reply was the echo of his own voice.

_"Shepard"_

He whirled around to see a ghostly, black silhouette coalesce out of thin air.

"Who are you?" He said suspiciously, no trace of fear in his voice.

_"Have you so easily forgotten me, Shepard? After all I was to you?"_ The ghost whispered as it drifted closer. _"Was I really anything to you if you can forget me so easily? After all we went through?"_

The black mist parted to reveal an attractive brunette, her long hair swept behind her head and her brown eyes trained on his.

And it all came back to him. Virmire, the Council, Saren, Sovereign, Wrex, the Normandy, the Reapers.

His death.

"A-Ash? How are you…?_" _He stammered uncertainly.

_"I'm dead, Shepard. Don't you remember?" _she whispered, _"You killed me"_

"Ash, please" He said, reaching for her "I didn't want…"

_"You killed __**ALL OF US**__!" _She suddenly screamed at him. She backhanded him, sending him flying backwards. His flight was stopped short by a tree, a sickening crack accompanying a sharp, burning pain stabbing into his back. He staggered up, blindingly trying to find her again through the pain. His body felt like it was on fire.

He staggered back in horror as he saw black silhouettes rising from the ground all around him. Each one had a face that he recognized. The faces that haunted his nightmares every time he slept, the faces that had driven him into insanity and depression, the faces that he felt watching him, judging him, in every second that that he had lived since they died.

The faces from Akuze.

They were joined by his crew from the Normandy. Garrus, Kaidan, Wrex, Ashley, Liara, and… Tali.

They crowded around him, endlessly screaming and wailing.

_"You let us die, Shepard!"_

_"Why didn't you do anything?"_

_"I'll never see my family again, because of you!"_

_"You should have died with us!"_

_"Everyone with you always dies, Shepard!"_

He curled into a ball as they came ever closer. Tears streaked down his cheeks as he heard their accusations. He tried to explain, to apologize, but all that came out was a broken sob.

_"Shepard! Shepard! Shepard! Shepard! Shepard!"_

Through all this, he saw one figure rise above the others. He blood turned to ice as recognition swept through him.

_"My death was nothing, Shepard. The Reapers are coming. You cannot stop them. No one can. They will destroy everything, as they have for millions of years. You failed, Shepard" _Saren Arterius whispered, his eyes a burning red and his cybernetically-augmented body pulsing with a same, strange light.

The bodies crowded him, grabbing him with a thousand dead hands, blotting out the light and suffocating him in their closeness.

_"Shepard! Shepard! Shepard! Shepard! Shepard!"_

**_"Shepard! Wake up!"_**

And he did.

* * *

"Shepard, do you hear me? Get out of that bed now – this facility is under attack"

The words came calmly but urgently from a communications device in his ear. Another explosion shook the room, and Shepard opened his eyes sleepily. He grunted and propped himself up on one elbow and grabbed his side as long-unused muscles protested the movement. He gingerly felt his cheek, where it burned like there were hot coals on it. He hissed from the lance of pain it brought him.

"Shepard, your scars aren't healed, but I need you to get moving. This facility is under attack" The voice repeated.

Sure enough, he could see gunfire on the other side of two windows set into the opposite wall from his position. He was lying on a sterile white operating table, surgical robotic limbs suspended above him from a module attached to the ceiling.

"There's a pistol in the locker on the other side of the room, Hurry!"

Shepard swung his legs down to the floor and steadied himself on the edge of the bed as his legs threatened to buckle. He limped toward the locker the voice had mentioned. He almost fell as he reached it, but steadied himself on the locker with both hands. He took several deep breaths, letting the pain in his muscles subside to a dull ache before he continued. He opened the locker and picked up the pistol.

"Who is this?" He said to the woman on the other end.

"It doesn't matter right now, get the pistol" ,the woman urged.

"This pistol doesn't have a thermal clip," He said, noticing the empty chamber.

"It was supposed to be a back-up. There should be some lying around somewhere"

Shepard looked around, but did not see any orange-lined cylinders. "There aren't any thermal clips here!"

"Shepard, they're going to blast through the door! Get to cover!" she said, ignoring him.

Shepard heard a _clunk_ as something hit the other side of the door at the other end of the room. He dove behind a crate just as an explosion threw the doors into the room, hurtling through the space he had just occupied, before coming to rest against the opposite wall.

He peeked around the corner and saw two thin, white robots enter and survey the room. They held their pistols stiffly in front of them. Artificial eyes swept the room and immediately turned toward Shepard's hiding place and opened fire. Shepard shrank back as shots hit all around him, but thankfully none impacting their target. He waited as they advanced until they were almost upon him before he stepped out and grabbed the closest one, keeping its pistol pointed away from him as he used it as a shield to block the other robot's shots.

One of the bullets hit home in his thigh and he gasped at the pain before charging the other robot with the now dead one in his hands and threw it, knocking it off its feet and onto the ground, its comrade trapping it as it feebly tried to continue its programming.

Shepard took his pistol and kept smashing at the mech's face until it stopped moving. He stopped for a moment to catch his breath and willed the pain away before grabbing its dropped pistol and limping through the door.

The woman guided him through the facility, telling him where to go,when to stop and hide, and when to move. A shootout was a last resort, the voice explained to him, because you are too valuable to be lost.

Shepard didn't understand what was going on, but he was clearly in danger, so he followed the woman's instructions without question.

At least until he got some answers.

Shepard was torn out of his thoughts as static began to erupt in his comms and he tried to make out what the woman was trying to tell him next, but it was too garbled.

There was nothing he could do about it, so he continued forward. He came upon a room with several terminals on various desks; one had an audio recording ready to play. Out of curiosity, he played the recording. Perhaps he would get some answers. His eyes widened as the recording played. The creator had talked about his concern of a _four billion_ credit spending for a 'Project Lazarus'.

Another terminal had a video, and showed a dark-haired woman talk about bio-synthetic fusion in an effort to accelerate reconstruction. _Reconstruction of what? _He wondered.

Shepard continued down the corridor as he pondered just what was going on.

* * *

Jacob launched another ball of blue energy at the attacking mechs and ducked back into cover. The ball detonated in the midst of them, sending the last of the attacking mechs crashing into the walls to lie in broken heaps while an unlucky few were disintegrated outright.

He fought to get his wind back; his extended use of his biotics was taking its toll on his body. As his breathing slowed, he heard the door behind him cycle open. He trained his gun on the corner where he knew the mechs would come from and steadied himself. If he was going to die today, he was going to take as many of these metal sons-of-bitches as he could with him.

* * *

Shepard opened the door just in time to hear gunshots that suddenly died as something detonated. Not as powerful as the previous ones he'd heard, this was explosion was more localized. He brought his pistol to bear and rounded the corner quickly, intending to take any hostiles nearby by surprise.

Instead he was met with a gunshot and bullet a bullet driving into his shoulder.

It spun him backwards and knocked him into a nearby wall. He sank into a sitting position and clenched his teeth against the pain.

He heard someone swear as they ran over and knelt next to him. Shepard feigned unconsciousness, a plan forming in his mind. He waited until he felt an arm checking his vitals and sprang into action, grabbing the arm and flipping his assailant onto his back, driving his knee into the man's chest and pinning the man's arm at a painful angle. His pistol pressed under the man's chin.

Now Shepard got a good look at his attacker. He was an African-American man with close-cropped hair and black bodysuit edged in yellow. On his left breast was an achingly familiar symbol, but he couldn't quite recall what it was.

"Whoa, wait, wait, wait!" The man said as he felt the pistol pressing into his jaw. The man put his free arm up in a nonthreatening gesture.

Shepard eased the pistol slightly.

"Where am I and how am I alive?" Shepard asked shakily.

The man took a deep breath before answering.

"All I can tell you is that you're in a space station. As to how you're alive, I'll leave that to the eggheads. I'm just a security guard, the name's Jacob Taylor" The man tried to smile, but it turned into a wince from the knee pressed into his chest.

"Why did you shoot me?"

The man sighed "Honestly, I thought you were one of those mechs coming up behind me"

Shepard saw no sign of deceit in the man, and, after a moment, released him and stepped back. Jacob coughed and rose after a moment. "Glad that that's settled. Sorry about that shot; how's your shoulder?" Jacob asked.

Shepard looked down to shoulder and was surprised to see very little blood. He opened the hole wider in his shirt with two fingers and saw the bullet hole had already been sealed with coagulating blood. He moved his shoulder experimentally and felt no pain. He remembered the bullet in his leg and saw it, too, had already stopped bleeding and began to heal.

Jacob watched, clearly as surprised as Shepard.

"Well, that's impressive" He remarked.

Shepard nodded absently. "We should get moving"

"Alright" Agreed Jacob, "The shuttle hangar is-"

Suddenly Jacob's omni-tool lit up and a desperate voice called out.

"Check, Check, is anyone still on this frequency? Anyone out there? Hello?"

Jacob tapped his earbud and replied.

"Wilson? This is Jacob. I'm with Commander Shepard. We just took out a wave of mechs in D-Wing"

"Shepard's alive? How the hell…never mind. You need to get him out of there. Get to the service tunnels and head for the network control center"

"Roger that, Wilson. Stay on this frequency" Jacob replied.

He turned toward Shepard.

"C'mon, Commander, the service tunnels are this way"

Shepard nodded and let Jacob lead the way. He made sure to keep Jacob in front of him where he could see him. He still didn't trust this man.

* * *

Jacob finished off another mech and popped a fresh thermal clip into his pistol. He keyed his comms.

"Dammit, Wilson, try to find us a way around these mechs. This is the third squad we've run into!"

Shepard looked at the still bodies of half a dozen hacked security mechs and felt a familiar sensation in his gut. Something didn't add up here.

"I'm trying, Jacob, I…wait…oh no…they've found me! Help!" Wilson screamed over the comms.

"Where are you, Wilson?"

"Server room B! Hurry!"

Jacob gestured to Shepard and they broke into a run towards the server room. Thankfully they met no other mech squads and entered the server room to see a bald man with a rough beard lying against a wall, bleeding from a gunshot wound in his leg. He looked up as they entered and grimaced.

"Bastards got me in the leg" He said, gesturing to his wound.

"Wilson?" Shepard said, "You look familiar"

"Yeah, I was part of the project to rebuild you. If you don't mind, can we talk about this _after_ we fix my leg?"

Jacob rose from checking Wilson's wound and nodded toward a terminal set in the wall across the room with a red cross on it.

"There should be some medi-gel in that dispenser there"

Shepard grabbed the clear paste and applied it to Wilson's wound, dabbing what was left on his own rapidly-healing bullet wounds.

Wilson noticed his action. "Did you get shot?"

"I'm fine" Shepard said stiffly.

Wilson glared at Jacob. "You were supposed to keep him safe! That is the only reason you're here! You-"

Jacob opened his mouth to protest but Shepard cut him off by grabbing Wilson's collar and lifting him into the air one-handed. Wilson visibly wilted when he saw Shepard's look.

"Listen, asshole, I just woke up, the last thing I remember was dying as my ship and my friends were destroyed by an enemy that came out of nowhere and matched no known records. I want to know why I'm alive again and my patience is wearing thin. Now get me the hell out of here so I can figure out why the hell I'm not dead" He hissed. His burning pain of his cheek increased and Wilson's eyes widened.

"Uh…yeah, yeah, the shuttles should be that way" Wilson gestured shakily.

Shepard dropped Wilson and let him lead the way toward the shuttle hangar. As he walked Wilson tried to explain his mysterious survival.

"I was trying to shut down the security mechs in the server room, but someone fried the whole system. Completely irreversible" He said.

Jacob squinted suspiciously. "We didn't ask what you were doing. And how do you have security mech clearance? You were in the bio wing"

"Weren't you listening? I was trying to help! Besides, I was shot! How do you explain that?" Wilson said, growing agitated.

"Yeah, Alright," Jacob said. Shepard could see him trying to piece the puzzle together. His own instincts told him not to trust Wilson.

"Wait" Said Jacob, stopping, "We need to find Miranda first. We can't leave her behind"

Wilson turned his head, continuing to walk on, "Forget about her. She was in D-Wing, and that place is overrun with security mechs. There's no way she survived"

"A bunch of mechs wouldn't stop Miranda. We need to find her", Jacob protested.

"If we look for her, there's a good chance we get killed. We need to save ourselves!" retorted Wilson. "Besides, we're almost to the shuttle bay!"

A moment of silence was broken by Jacob.

"Shepard" Jacob said. Shepard paused, and, after a moment, Wilson followed suit.

"If I tell you who we work for, will you trust us more?" He asked.

"This really isn't the time, Jacob" Wilson said urgently.

"We can't go on like this, with Shepard expecting a shot in the back. Shepard…the project the rebuilt you, the Lazarus Project … is funded and controlled by Cerberus"

Shepard's pistol was instantly in his hand before either of them could react.

"Whoa, whoa!" cried Wilson, putting his hands into the air. Jacob, to his credit, didn't flinch.

"Cerberus," Spat Shepard, "Why the hell would Cerberus bring me back?"

Jacob crossed his arms. "That's not for me to say, Commander, but I need you to trust us. The Alliance declared you dead; Cerberus spent billions to bring you back. I'd be suspicious too, but I felt you deserve to know what's what. After we get out of here, I can take you to the Illusive Man. He'll explain everything"

Shepard remembered the atrocities he had seen that Cerberus had committed. The most vivid was Admiral Kahoku, his lifeless body covered with needle marks, lying deep in an underground Cerberus facility after trying to figure out who was behind the death of his men. No man should die like that.

Shepard's grip tightened on the pistol. He should gun them down right now, but they were the only ones who could get him off the station. After another tense moment he relented and holstered his pistol. Jacob breathed a sigh of relief he didn't know he had been holding.

"This isn't over" Shepard said as he pushed past them.

Wilson, still terrified, glared at Jacob again before following Shepard. Jacob sighed before he, too followed.

* * *

The few mechs that had occupied the shuttle bay had been quickly and easily disposed of.

"Over here!" Wilson waved them over to a door. It opened into a small airlock, with an identical door at the other end. Wilson moved to the other door.

"The shuttle pad is right through here…" He said as he keyed the door control.

The door hissed open to reveal a woman standing just on the other side. She had jet black hair that cascaded down to her shoulders, her body wrapped in a form-fitting bodysuit that accentuated her curves.

Wilson looked surprised "Miranda? But you were-"

Miranda cut him off with a shot to the face.

Shepard's own weapon was trained on Miranda even before Wilson's body had hit the floor.

"Dead?" Miranda finished, contempt twisting her face as she regarded Wilson's body.

"What the hell are you doing?" Jacob said, stunned by the turn of events.

"My job. Wilson betrayed us all" Miranda said, still looking at Wilson's body with distaste.

Shepard lowered his pistol slightly "I knew something didn't add up. Still, an interrogation would have been more useful than an execution"

"No time" Miranda said brusquely "My boss wants to speak to you", she said, looking at him.

Miranda's look of distaste now transferred to Shepard.

"The Illusive Man? I know who, and what, you work for"

Miranda looked at Jacob. "Ah, Jacob. I should've known your conscience would get the better of you"

Jacob shifted uneasily but his voice was steady. "Lying to the Commander is not the way to get him to join our cause"

"Fair point," Miranda conceded, "Since we're getting everything into the open, is there anything else you'd like to know, Commander?"

"Just why the hell you resurrected me" He replied vehemently.

A look of amusement crossed her face. "I'll leave that to the Illusive Man to explain"

He put his pistol away as she started moving to an idling shuttle nearby.

"Wait" He said.

She sighed and turned back, "Yes?"

"Did anyone make it?" He asked.

She looked confused before realizing what he meant. "I'm sorry, Commander" she said.

"Nobody survived"

* * *

**A/N: So that's it. I'll continue, but I may not be able to upload them on a timely basis, what with school starting. I'll try for bi-weekly, or monthly at the max.**

**P.S. Don't worry, the Talimance is coming in the next chapter. At least the first part :)**

**~Kraretyer**


End file.
